Acid rain is a serious environmental problem and has obvious impacts on the growth, reproduction, and photosynthesis of terrestrial plants. Ulva prolifera, a main blooming species of green tides, was studied on its physiological response to acid rain. The photosynthetic parameters were determined under different conditions (salinity: 1, 10, 30‰; pH: 3.0, 3.5, 4.5; duration: 0.5, 1.0, 2.0 h) followed by 24-h recovering under natural conditions. Results showed 1-h treatment with pH 3.5 caused 50-70% reduction in the maximal quantum yield of PSII photochemistry (Fv/Fm) and effective quantum yield of PSII photochemistry (ФPSII) at normal salinity but when the low pH was combined with a salinity of 10‰ or lower, PSII activity was almost completely inhibited. Moreover, the low salinity (1‰ and 10‰) reduced the degree of photoprotection under low pH (3.5) conditions. Finally, we speculated if the pH of acid rain ≤ 3.5, with 1‰ salinity and 2-h rainfall time, the amount of U. prolifera and the scale of green tides would decrease.